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Protocol for assessing distances in pathway space for classifier feature sets from machine learning methods.

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Title: Protocol for assessing distances in pathway space for classifier feature sets from machine learning methods.
Authors: Tercan B; Institute of Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA. Electronic address: btercan@systemsbiology.org., Apolonio VH; Bioinformatics and Systems Biology Laboratory, Federal University of Paraná, Curitiba, PR 81520-260, Brazil., Chagas VS; Bioinformatics and Systems Biology Laboratory, Federal University of Paraná, Curitiba, PR 81520-260, Brazil., Wong CK; UC Santa Cruz Genomics Institute and Department of Biomolecular Engineering, Santa Cruz, CA 95060, USA., Lee JA; Oregon Health and Science University, Portland, OR 97239, USA., Yau C; University of California, San Francisco, Department of Surgery, San Francisco, CA 94158, USA; Buck Institute for Research on Aging, Novato, CA 94945, USA., Benz CC; Buck Institute for Research on Aging, Novato, CA 94945, USA., Stuart JM; UC Santa Cruz Genomics Institute and Department of Biomolecular Engineering, Santa Cruz, CA 95060, USA., Karlberg BJ; Oregon Health and Science University, Portland, OR 97239, USA., Ellrott K; Oregon Health and Science University, Portland, OR 97239, USA., Grewal JK; Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada., Jones SJM; Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada., Zenklusen JC; Center for Cancer Genomics, National Cancer Institute, Bethesda, MD 20892, USA., Robertson AG; Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada., Laird PW; Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA. Electronic address: peter.laird@vai.org., Cherniack AD; The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02115, USA. Electronic address: achernia@broadinstitute.org., Castro MAA; Bioinformatics and Systems Biology Laboratory, Federal University of Paraná, Curitiba, PR 81520-260, Brazil. Electronic address: mauro.castro@ufpr.br.
Corporate Authors: Cancer Genome Atlas Analysis Network
Source: STAR protocols [STAR Protoc] 2025 Jun 20; Vol. 6 (2), pp. 103681. Date of Electronic Publication: 2025 Mar 18.
Publication Type: Journal Article
Journal Info: Publisher: Cell Press Country of Publication: United States NLM ID: 101769501 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 2666-1667 (Electronic) Linking ISSN: 26661667 NLM ISO Abbreviation: STAR Protoc Subsets: MEDLINE
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  Data: <searchLink fieldCode="AU" term="%22Tercan+B%22">Tercan B</searchLink>; Institute of Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA. Electronic address: btercan@systemsbiology.org.<br /><searchLink fieldCode="AU" term="%22Apolonio+VH%22">Apolonio VH</searchLink>; Bioinformatics and Systems Biology Laboratory, Federal University of Paraná, Curitiba, PR 81520-260, Brazil.<br /><searchLink fieldCode="AU" term="%22Chagas+VS%22">Chagas VS</searchLink>; Bioinformatics and Systems Biology Laboratory, Federal University of Paraná, Curitiba, PR 81520-260, Brazil.<br /><searchLink fieldCode="AU" term="%22Wong+CK%22">Wong CK</searchLink>; UC Santa Cruz Genomics Institute and Department of Biomolecular Engineering, Santa Cruz, CA 95060, USA.<br /><searchLink fieldCode="AU" term="%22Lee+JA%22">Lee JA</searchLink>; Oregon Health and Science University, Portland, OR 97239, USA.<br /><searchLink fieldCode="AU" term="%22Yau+C%22">Yau C</searchLink>; University of California, San Francisco, Department of Surgery, San Francisco, CA 94158, USA; Buck Institute for Research on Aging, Novato, CA 94945, USA.<br /><searchLink fieldCode="AU" term="%22Benz+CC%22">Benz CC</searchLink>; Buck Institute for Research on Aging, Novato, CA 94945, USA.<br /><searchLink fieldCode="AU" term="%22Stuart+JM%22">Stuart JM</searchLink>; UC Santa Cruz Genomics Institute and Department of Biomolecular Engineering, Santa Cruz, CA 95060, USA.<br /><searchLink fieldCode="AU" term="%22Karlberg+BJ%22">Karlberg BJ</searchLink>; Oregon Health and Science University, Portland, OR 97239, USA.<br /><searchLink fieldCode="AU" term="%22Ellrott+K%22">Ellrott K</searchLink>; Oregon Health and Science University, Portland, OR 97239, USA.<br /><searchLink fieldCode="AU" term="%22Grewal+JK%22">Grewal JK</searchLink>; Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada.<br /><searchLink fieldCode="AU" term="%22Jones+SJM%22">Jones SJM</searchLink>; Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada.<br /><searchLink fieldCode="AU" term="%22Zenklusen+JC%22">Zenklusen JC</searchLink>; Center for Cancer Genomics, National Cancer Institute, Bethesda, MD 20892, USA.<br /><searchLink fieldCode="AU" term="%22Robertson+AG%22">Robertson AG</searchLink>; Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada.<br /><searchLink fieldCode="AU" term="%22Laird+PW%22">Laird PW</searchLink>; Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA. Electronic address: peter.laird@vai.org.<br /><searchLink fieldCode="AU" term="%22Cherniack+AD%22">Cherniack AD</searchLink>; The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02115, USA. Electronic address: achernia@broadinstitute.org.<br /><searchLink fieldCode="AU" term="%22Castro+MAA%22">Castro MAA</searchLink>; Bioinformatics and Systems Biology Laboratory, Federal University of Paraná, Curitiba, PR 81520-260, Brazil. Electronic address: mauro.castro@ufpr.br.
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